Factual error: A flight manifest would never state on its seating chart that an armed U.S. marshal was on board as it gives away that person's identity and puts everyone on board in danger.
Factual error: The crew sent to board the ill fated jumbo jet is in the "Remora", which is clearly a modified F-117A Stealth Fighter, but retaining the same dimensions. It would be physcially impossible to fit that many people and such a spacious cargo hold into a plane that size with the engines. In fact, with the additional weight, the engines would have to be even bigger for it to operate.
Factual error: Computerized maps throughout the movie show the plane heading due west past Spain and Portugal from Athens to Washington, D.C. Aircraft follow great circle route; although Athens and DC are similar in latitude, the shortest flight path is north over Scandinavia. No commercial air route between Athens and the East Coast fly over Spain.
Factual error: When the bullet is fired through the aircraft window there would be no possible way that Grant would be able to hold on for that whole time as the plane is travelling up to 600mph and also his temperature will lower immediately, which would cause weakness.
Factual error: When John Leguizamo is surveying the cabin for terrorists and reporting back to Kurt Russell, he says the terrorists are carrying 9mm Skorpions. The Skorpion IS produced in 9mm Makarov and .380 Auto versions, but those weapons have straight magazines, not curved ones. The terrorists' Skorpions have curved magazines, which denotes the weapon being chambered for 7.65 Browning.
Factual error: As they are disarming the bomb, the hard drive on the bomb has no cover. A speck of dust would destroy an exposed hard drive and it would never be used exposed like that. As Cahill is a design engineer and quoted as being able to build computers, he should know that this hard drive is wrong.
Factual error: Kurt Russell lands the 747 at Frederick field and during the rollout the plane's left engines collide with parked aircraft and it finally runs off the departure end of the runway into a sand drag. While it is true that the 5000 ft runway at Frederick field is too short for a Boeing 747 in reality there would not be aircraft parked so close to a runway at any airport, and we know that the 747 did not veer off the runway since it struck approach lights at both ends of the runway.
Factual error: Throughout the movie the Carrier mentioned that will send fighters to attack the Highjacked airliner is the CVN-69 Uss Dwight D. Eisenhower. You can see CVN-69 on the briefing screen at the NMCC. However after the SECDEF gets the pic of the bombmaker they cut to a scene of the carrier getting her fighters ready and the carrier is now the CVN-74 Uss John C. Stennis. You can see the 74 on the tower of the carrier.
Factual error: When the fighter jets get ready to shoot down the jumbo jet from behind, Baker sends a Morse code message via the plane's rear lights to the fighter pilots. From such a short time of the fighter pilots viewing the message, they were able to immediately decode it as "Hail Mary, Alpha 1, 10 minutes. "Message repeats" says fighter jet pilot. Wouldn't it be impossible to send such an elaborate message via Morse, let alone be decoded so quickly and repeated in such a short time?